Proper control of epigenetic state is fundamental to human health, beginning with gametogenesis and continuing through fertilization, development and into adulthood. When normal epigenetic control is lost in the germline, the result is often sterility, when it is lost in somatic tissues after fertilization, essential processes such as cell differentiation, identity and function break down, which contributes to a multitude of disease states. Though many biochemical and genetic studies have identified trans-acting factors regulating the epigenome, and parallel epigenomic studies have identified where they have left their mark, there is a stark gap of knowledge in the middle regarding the mechanisms that control where the trans-acting factors are directed to place their epigenetic marks in the genome. The fundamental goal of this proposal is to define mechanisms by which epigenetic states are controlled at specific locations in the germline and after fertilization. Our previous studies identified a cis-acting mechanism that regulates DNA methylation in the male germline and during pre- implantation development at the differentially methylated region (DMR) of the imprinted mouse Rasgrf1 locus. The mechanism is novel and requires factors in the piRNA pathway, piRNAs transcribed from sequences unlinked to Rasgrf1, and an antisense transcript called the pit-RNA that spans the Rasgrf1 DMR and is itself processed into piRNAs. When pit-RNA transcription is misregulated, aberrant methylation occurs that can be transmitted to the normally unmethylated allele and to future generations, even if the misregulated allele is not itself transmitted. Three sets of studies are proposed in three Aims. The first will identify when during development pit-RNA expression is required for normal DNA methylation, when its mis-expression leads to epigenetic aberrations, and if transmission of the pit-RNA by gametes can influence epigenetic states in the next generation. The second will define the structural features the pit-RNA must have for it to control DNA methylation. The third will use genetic and biochemical approaches to identify factors that interact and collaborate with the pit-RNA to mediate its methylation-regulating activity. These studies make use of one of the most tractable systems for studying is acting mechanisms controlling epigenetic states in the germline and somatic tissues, both within and between generations in mammals. Such studies are fundamental to understand how epigenetic states are controlled and will identify critical points of regulation where this control can go awry in human disease.